Life in the Third Realm

Fernley | Dreamstime.comArchaea were first found in areas like Bumpass Hell in Lassen Volcanic National Park, where fissures and volcanic heat created hot springs.

It’s that time of the month again. Yes: it’s time for Life-form of the Month. In case you’ve forgotten, this coming Saturday is International Day for Biological Diversity, a day of celebrations and parties to appreciate the other occupants of the planet. So if you do nothing else this weekend, drink a toast to “Other Life-forms!” In honor of this event, my nomination for Life-form of the Month: May is a group of abundant and fascinating beings that are undeservedly obscure: the archaea.

Say who?

Archaea are single-celled microbes with a reputation for living in tough environments like salt lakes, deep sea vents or boiling acid. One strain can grow at temperatures as high as 121 degrees Celsius (249.8 degrees Fahrenheit), a heat that kills most organisms; others thrive at the seriously acidic pH of zero.

They are not restricted to life at the fringes, however. As we have learned how to detect them, archaea have turned up all over the place. One survey estimated that they account for as much as 20 percent of all microbial cells in the ocean, and they’ve been discovered living in soil, swamps, streams and lakes, sediments at the bottom of the ocean, and so on. They are also routinely found in the bowels of the Earth — and the bowels of animals, including humans, cows and termites, where they produce methane. Indeed, the archaeon known as Methanobrevibacter smithii may account for as much as 10 percent of all the microbial cells living in your gut.
But here’s the thing. The tree of life falls into three big lineages, or realms of life. (Confession: the technical term is “domains,” not “realms,” but I’m taking poetic license.) The most familiar realm comprises the eukaryotes — which is the blanket term for most of the organisms we are familiar with, be they mushrooms, water lilies, tsetse flies, humans or the single-celled beasties that cause malaria. Eukaryotes have many distinguishing features, including the fact that they keep their genes in a special compartment known as the cell nucleus.

The second member of the trinity is made up of bacteria. We tend to associate bacteria with disease — for they can cause a range of nasty infections, including pneumonia, syphilis, leprosy, tuberculosis and the like. But in fact, most bacteria lead blameless lives (some of which I have written about in previous columns). There are many differences between eukaryotes and bacteria; but one of the most obvious is that bacteria do not sequester their DNA in a cell nucleus.

Courtesy NASA/JPL-CaltechMethanogens, a type of archaea.

The third great lineage of living beings is the archaea. At first glance, they look like bacteria — and were initially presumed to be so. In fact, some scientists still classify them as bacteria; but most now consider that there are enough differences between archaea and bacteria for the archaea to count as a separate realm.

The most prominent of these differences lies in the structure of the ribosome — the piece of cellular machinery that is responsible for turning the information contained in DNA into proteins. Indeed, it was the discovery of the archaeal ribosome by the biologist Carl Woese in the 1970s that led to their being recognized as the third branch of the tree of life.

What else sets them apart? They sometimes come in peculiar shapes: Haloquadratum walsbyi is rectangular, for example. Some archaea are ultra-tiny, with cell volumes around 0.009 cubic microns. (For comparison, human red blood cells have a volume of around 90 cubic microns. A micron is a millionth of a meter — which is extremely small.)

More diagnostic: archaeal cell membranes have a different structure and composition from those of bacteria or eukaryotes. And although archaea organize their DNA much as bacteria do (they also have no cell nucleus, for example), many aspects of the way the DNA gets processed are distinctly different. Instead, the processing is more similar to what goes in within eukaryotic cells. Archaea also have large numbers of genes that are not found in the other groups.

But to me their most telling feature is that they have their own set of extremely weird viruses. Not only do archaeal viruses also come in odd shapes — some of them look like little bottles — but the set of genes they have is unlike that of viruses that parasitize bacteria or eukaryotes. In other words, viruses can also be divided into three big groups: those that attack bacteria, those that attack eukaryotes and those that attack archaea.

The archaea still hold many mysteries. Few of them can be grown in the laboratory, so they are hard to study in detail; many of them are known from their DNA alone. Moreover, their exact position on the tree of life — when they evolved relative to the other two groups — remains disputed. Yet it may be that archaea feature in our ancestry: according to one view, eukaryotes themselves evolved from an ancient fusion between a bacterium and an archaeon.

But whether this is the case, or whether they are merely co-occupants of the planet, let’s hear it for these Other Life-forms!

Notes:

For a delightful introduction to the archaea, see Howland, J. L. 2000. “The Surprising Archaea: Discovering Another Domain of Life.” Oxford University Press. For a more technical overview, see Cavicchioli, R. (editor). 2007. “Archaea: Molecular and Cellular Biology.” ASM Press. See page 21 for a photograph of the square archaeon, Haloquadratum walsbyi; this book also contains detailed descriptions of how archaea differ from eukaryotes and bacteria.

For archaea thriving at temperatures of 121 degrees C, see Kashefi, K. and Lovley, D. R. 2003. “Extending the upper temperature limit for life.” Science 301: 934. For archaea growing at zero pH, see Fütterer, O. et al. 2004. “Genome sequence of Picrophilus torridus and its implications for life around pH 0.” Proceedings of the National Academy of Sciences USA 101: 9091-9096.

Descriptions of eukaryotes and bacteria can be found in any general biology textbook. For the view that archaea are merely a type of exotic bacteria, see page 123 of Cavalier-Smith, T. 2010. “Deep phylogeny, ancestral groups and the four ages of life.” Philosophical Transactions of the Royal Society B 365: 111-132. For a robust account of the three branches view of the tree of life, see for example, Pace, N. R. 2009. “Mapping the tree of life: progress and prospects.” Microbiology and Molecular Biology Reviews 73: 565-576.

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Olivia Judson, an evolutionary biologist, writes every Wednesday about the influence of science and biology on modern life. She is the author of “Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex.” Ms. Judson has been a reporter for The Economist and has written for a number of other publications, including Nature, The Financial Times, The Atlantic and Natural History. She is a research fellow in biology at Imperial College London.